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Publication for RBPmotif
RNA Binding Protein Vigilin Collaborates with miRNAs To Regulate Gene Expression for Caenorhabditis elegans Larval Development
[…] miRNAs and families of miRNAs in regulating the first larval stage of C. elegans development.Although we were not able to determine a high confidence VGLN-1 binding motif using computational methods [RBPMotif ()], the enrichment of specific miRNA target sites among VGLN-1 target mRNAs could suggest that alternative methods of functional selectivity may exist. This enrichment and genetic interactio […]
Revealing protein–lncRNA interaction
[…] context of motif discovery at RBP binding sites can be found in . The already mentioned MEMERIS , CMfinder , RNApromo , StructRED , the algorithm by Li and collaborators , RNAcontext and RBPmotif [, ], GraphProt  and Zagros  are all tools that use, with different strategies and to different extent, secondary structure information to determine more specific binding motifs.The appli […]
High throughput characterization of protein–RNA interactions
[…] condary structure context (e.g. a hairpin loop) and learns the weights for each position from a set of input sequences annotated with relative binding affinity . RNAcontext is also available on the RBPmotif Web server .The second approach considers RNA secondary structure explicitly and includes stochastic context-free grammar (SCFG) and graphical approaches. CMfinder  and RNApromo  both s […]
Finding the target sites of RNA binding proteins
[…] binding affinities of the RBP of interest. Each input RNA sequence is scored by using the sequence and structure context parameters. RNAcontext has been applied to in vitro binding-affinity data. The RBPmotif webserver implements RNAcontext. […]
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